There is provided a batch type heat treatment system, control method and heat treatment method capable of appropriately coping with a multi-product small-lot production. A reaction tube 2 comprises a plurality of heaters 31 through 35 and a plurality of temperature sensors, and houses therein a wafer boat 23. A control part 100 stores therein many mathematical models for estimating (calculating) the temperature of wafers W in the reaction tube 2, in accordance with the number and arranged position of the wafers W mounted on the wafer boat 23, and many target temperature trajectories. If the wafer boat 23 is loaded in the reaction tube 2, a mathematical model and a target temperature trajectory corresponding to the number and arranged position of the mounted wafers W are read. If a deposition process is started, the output of a temperature sensor S and the model are used for estimating the temperature of the wafers W in the reaction tube 2, and the powers to be supplied to the heaters 31 through 35 are separately controlled so that the estimated temperature approaches the target temperature trajectory.